The 27-year-old, who impressed in the U.S. side's run to the Confederations Cup final last month, has joined on a free transfer from Standard Liege and penned a three-year contract.
The club announced the signing on their website and pointed out he holds a Belgian passport, which means Onyewu will not count as one of only two non-EU players Italian sides are allowed to sign each season.
Milan's interest in the defender had barely been mentioned in the media and his signing comes just a day after hundreds of fans protested at the first day of pre-season training.
Ultra fans chanted slogans and unveiled banners criticising owner Silvio Berlusconi and the decision to sell playmaker Kaka to Real Madrid for 67 million euros.
The Rossoneri, who lost coach Carlo Ancelotti to Chelsea having finished third in Serie A last season, had previously only signed Brazil defender Thiago Silva and little-known young players.
They are seeking a new striker with Real forward Klaas Jan Huntelaar, Sevilla's Luis Fabiano, Arsenal striker Emmanuel Adebayor and VfL Wolfsburg's Edin Dzeko in the frame.
Onyewu could end up partnering Silva in central defence given captain Paolo Maldini retired at the end of last season and Alessandro Nesta and Kakha Kaladze are injury prone.
Milan, now coached by rookie Brazilian Leonardo, have also announced that midfielder Massimo Ambrosini will be the new captain.
